Aligments for a candidate for ams in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for ams in Shewanella sp. ANA-3

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 7025148 Shewana3_2311 alpha amylase, catalytic region (RefSeq)

Query= uniprot:H3K096
         (538 letters)



>lcl|FitnessBrowser__ANA3:7025148 Shewana3_2311 alpha amylase,
           catalytic region (RefSeq)
          Length = 540

 Score =  643 bits (1659), Expect = 0.0
 Identities = 298/529 (56%), Positives = 376/529 (71%), Gaps = 3/529 (0%)

Query: 5   MMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFG 64
           + WWRG VIYQIYPRS LD+ GDGVGDL GI  KLDY+ASLNVD IW+SPFF SPM DFG
Sbjct: 4   LTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFG 63

Query: 65  YDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPK 124
           YD+SDYR+VDP+FGT++DF  L+EKAH  G+KV+IDQV+SHTSDQH WF ESR++RTNPK
Sbjct: 64  YDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRTNPK 123

Query: 125 ADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQ 184
           ADW+VWA+PK DGT PNNWL+IFGG AW ++ RRQQYYLHNFL SQPD+NFH+P+ RQA 
Sbjct: 124 ADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAV 183

Query: 185 LDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDL 244
           LDN+ FWL  GVDGFRLD + F +HD +LRDNPP PK + +  G  E NPY +Q H Y+ 
Sbjct: 184 LDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHYYNN 243

Query: 245 SRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH 304
            RP+ + F+++LR L++ YPG  T+GE+  ++ L  MA YT G D+LHMAY+F+LL   +
Sbjct: 244 DRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLTDDY 303

Query: 305 SASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGS 364
           SA+Y+R+ +E  +   GD WPCWA  NHD  R A+RWG  +      K++ A++ SLRGS
Sbjct: 304 SAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGRGKQTSDMVKMLNAMVNSLRGS 363

Query: 365 VCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPW 423
           VC YQGEELGL EA + +  +QDP+GK  WP FKGRDGCRTPMPW  + +  GFS V PW
Sbjct: 364 VCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFSGFSQVTPW 423

Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQK 483
           LP+   H  LAV  Q+ D  + L+  R  LA+R+ +PAL +G++  +D  + LL F R  
Sbjct: 424 LPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEPLLVFVRTS 483

Query: 484 GDETLLCVFNLTGQEQQTTLPVEVASDLPVAH--FTATRDGSTLTLPAY 530
           G++ LL  FNL   EQ  +L           H   TA R   TLT  AY
Sbjct: 484 GEQKLLVCFNLQDTEQALSLDALSIQQEITGHGLKTAQRIADTLTFSAY 532


Lambda     K      H
   0.320    0.138    0.443 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 946
Number of extensions: 40
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 538
Length of database: 540
Length adjustment: 35
Effective length of query: 503
Effective length of database: 505
Effective search space:   254015
Effective search space used:   254015
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources